Fix multiscale examples

[jo-mueller]

Mirror PR to carry ome/ngff#311 over to ngff-spec. Can be merged once that ome/ngff#311 has been merged, too, to make sure both places stay in sync and that @mkitti's contribution is acknowledged in the commit history.

Co-pilot description

This pull request updates several NGFF multiscales example JSON files to standardize dataset path naming and improve the representation of coordinate systems and transformations. The most significant changes include renaming dataset paths from numeric values to string identifiers (e.g., "0" → "s0"), updating transformation input references accordingly, and enhancing the structure for specifying coordinate systems in the multiscales metadata.

Standardization of dataset paths and input references:

• Changed dataset path fields from numeric strings (e.g., "0", "1", "2") to string identifiers ("s0", "s1", "s2") in multiscales_example.json, multiscales_example_relative.json, and multiscales_transformations.json. Updated all corresponding input fields in coordinateTransformations to match the new path names. [1] [2] [3] [4]

Enhancements to coordinate system specification:

• Added a coordinateSystems section to the multiscales metadata in multiscales_transformations.json, explicitly defining the "intrinsic" coordinate system and its axes. [1] [2]

Other metadata improvements:

• Updated the multiscales name field in multiscales_transformations.json from "image_with_coordinateTransformations" to "image_with_multiscaleTransformations" for clarity and consistency.

[github-actions]

Automated Review URLs

• Readthedocs

[mkitti]

The comments here are higlighted in red when viewed on Github because the comments are invalid in JSON. Would it make sense to change the extension for this to .jsonc or .json5 since JSONC and JSON5 do allow for comments?

In the markdown, the language is marked as json as well.

[jo-mueller]

Hi @mkitti , no strong opinion here. In the markdown documents, jsonc metadata are flagged as jsonc documents like this:

```jsonc
{
  // ...
  "attributes": {
    "ome": {
      "version": "0.5",
      // ...
    }
  }
}
```

Tbh, I wasn't even aware that .jsonc is a valid extension for JSON files :)

[will-moore]

ome/ngff#311 and my duplicated version of this at #56 both had changes to index.md which aren't in this PR.

[jo-mueller]

@mkitti can you check whether this sorts out all of the formatting issues you raised at ome/ngff#311?

@will-moore am I missing some more instances of malformating here? 🤔

[will-moore]

#56 had changes to index.md which are not included here and I think are useful (and some other file changes too)

[mkitti]

can you check whether this sorts out all of the formatting issues you raised at ome/ngff#311?

It does not. The examples have comments in what is labeled as JSON, which does not allow for comments.

[jo-mueller]

@will-moore would you mind merging #56 into this PR?

[will-moore]

@jo-mueller I don't mind it happening but I don't think I can push to this branch myself. I have re-opened that PR against this branch as jo-mueller#5